Phylogeography and historical introgression in Stickleback fishes Cui Wang Ecological Genetics Research Unit Faculty of Biological and Environmental Sciences University of Helsinki Finland Academic dissertation To be presented for public examination with the permission of the Faculty of Biological and Environmental Sciences of the University of Helsinki in Au- ditorium 2, Info Centre Korona (Viikinkaari 11), on 9th of March 2018 at 12.00 o’clock noon. Helsinki 2018 Supervised by Prof. Juha Merilä University of Helsinki, Finland Dr. Takahito Shikano University of Helsinki, Finland Thesis advisory committee Doc. Perttu Seppä University of Helsinki, Finland Dr. Helena Johansson University of Helsinki, Finland Pre-examiners Doc. Laura Kvist University of Oulu, Finland Asst. Prof. Robert Ekblom Uppsala University, Sweden Opponent Prof. Jacob Höglund Uppsala University, Sweden Custos Prof. Juha Merilä University of Helsinki, Finland Layout and cover by: © Cui Wang ISBN 978-951-51-4084-5 (paperback) ISBN 978-951-51-4085-2 (PDF) http://ethesis.helsinki.fi Unigrafia, Helsinki 2018 穷且益坚，不坠青云之志。老当益壮，宁移白首之心？ ——王勃 The more difficult it is, the stronger we need to be. Never give up your dream! Contents Abstract .............................................................................................................................. 6 1. Introduction ............................................................................................................... 8 1.1 Phylogeography and climate changes.................................................................. 8 1.1.1 Population genetics and climate changes ........................................................ 8 1.1.2 Phylogeography of freshwater fishes ............................................................... 9 1.1.3 Molecular markers and phylogeography ......................................................... 9 1.2 Study systems ...................................................................................................... 10 1.2.1 Taxonomy and distribution of Pungitius species ............................................ 10 1.2.2 Intraspecific genetic divergence of Pungitius species .................................... 11 1.2.3 Interspecific introgression among Pungitius species ..................................... 12 2. Aims of the thesis ..................................................................................................... 12 3. Materials and Methods ........................................................................................... 13 3.1 Study species and sampling ................................................................................ 13 3.2 Molecular markers ............................................................................................. 15 3.3 Statistical analyses ............................................................................................. 16 4. Results and discussion ............................................................................................. 20 4.1 Phylogeography of Pungitius species ................................................................ 20 4.2 Historical introgression among Pungitius species............................................. 24 4.3 Reproductive isolation between species ............................................................. 27 Conclusions and outlook ................................................................................................ 29 Acknowledgements ......................................................................................................... 30 References ........................................................................................................................ 31 The content of the dissertation is based on the following articles: I Cui Wang, Takahito Shikano, Henri Persat, Juha Merilä 2015. Mitochondrial phylo- geography and cryptic divergence in the stickleback genus Pungitius. Journal of Bi- ogeography 42: 2334-2348. II Cui Wang, Takahito Shikano, Henri Persat, Juha Merilä 2017. Phylogeography and historical introgression in smoothtail nine-spined sticklebacks, Pungitius laevis (Gas- terosteiformes: Gasterosteidae). Biological Journal of the Linnean Society 121: 340-354 III Baocheng Guo, Takahito Shikano, Cui Wang, Alexandra Kravchenko, Juha Merilä. A phylogenomic perspective to diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius. Submitted manuscript. The following table shows the contributions of authors to the original articles. The authors are referred to by their first initials, and the articles by their roman numer- als. I II III Original idea TS JM CW TS JM CW JM BG TS Sample collection JM HP TS HP TS JM JM TS AK BG Molecular data collection TS CW TS BG JM CW Data analyses CW TS CW TS BG Manuscript preparation TS CW JM HP CW TS JM HP JM BG CW TS AK: Alexandra Kravchenko HP: Henri Persat BG: Baocheng Guo JM: Juha Merilä CW: Cui Wang TS: Takahito Shikano Abstract Pleistocene glaciations have profoundly influenced the genetic diversity of organsims in the Northern Hemisphere. Large ice sheets covered vast areas of the Eurasian conti- nent, driving species southward to different isolated refugia, often resulting in deep di- vergences within species. Phylogeographic studies carried out on Pungitius species based on mitochondrial DNA (mtDNA) support profound intraspecific genetic divergence in refugia during glaciation cycles. However, compared to species distributed at lower lati- tudes, those distributed at higher latitudes may have also occurred in cryptic refugia in periglacial areas during glaciations, complicating the inferences of the phylogeographic patterns of the fish species with a circumpolar distribution, such as the Pungitius stickle- backs. Moreover, comprehensive phylogenetic studies of Pungitius species have been lacking in the sense that not all extant species have been included into analyses. In this dissertation, I carried out phylogeographic studies on seven Pungitius species using both mtDNA and genome-wide nuclear SNP markers, with worldwide sampling of popula- tions to shed light on intra- and interspecific divergence in this genus, as well as to study their historical demography and interspecific hybridization. By sequencing five mtDNA regions, I found six highly divergent Pungitius lineages including those corresponding to P. pungitius, P. platygaster, P. tymensis and P. kaiba- rae, and two independent monophyletic lineages of P. laevis. I also found a third lineage of P. laevis that clustered together with P. pungitius. To understand whether this cluster- ing of the P. laevis lineage III and P. pungitius mtDNA was a result of convergence or interspecific introgression, I conducted phylogeographic and population genetic analyses using both mtDNA and nuclear gene sequences. The results indicated asymmetric mito- chondrial introgression from P. pungitius to P. laevis and genetic admixture of these spe- cies. Hence, the results suggest that the P. laevis lineage III has experienced historical hybridization. Deep intraspecific mitochondrial divergence was found within P. laevis in central and southern France, coinciding with major drainages, suggesting that these areas correspond to distinct glacial refugia for the species explaining the observed intraspecific divergence. To further clarify evolutionary relationships between different Pungitius species and populations, as well as to study the prevalence and extent of introgression among recog- nized species, phylogenomic datasets were constructed from restriction-site associated DNA in combination with mitochondrial genomes. All divergences in the Western Pale- arctic were estimated to have occurred during the Pleistocene (≤ 2.6 Ma). The phyloge- netic patterns suggest a major split in Pungitius genus occurred early in history, resulting in an East Asian group (P. kaibarae, P. tymensis, P. sinensis) and European - North America group (P. hellenicus, P. platygaster, P. laevis and P. pungitius). The genus probably originated from the Western Pacific and spread to Europe and North America through the Arctic Ocean in several waves after the opening of the Bering Strait. Four cases of incongruence between nuclear and mtDNA-based trees revealed evidence for frequent hybridizations and mitogenome capture during the evolutionary history of this genus. Further analyses of these four cases of cytonuclear incongruence also revealed evidence for nuclear introgression, but the estimated levels of autosomal introgression were low. gent lineages within species. In fact, Qua- 1. Introduction ternary glaciations have been the most in- fluential climatic changes that have affect- 1.1 Phylogeography and climate ed the phylogeographic patterns of terres- changes trial organisms in the past few million years (Hewitt 2004). When ice sheets ac- 1.1.1 Population genetics and climate cumulated on the Northern Hemisphere changes during glaciations, most surviving animal The history of species in space and time populations retreated to southern refugia is a topic of continued interest for evolu- (Hewitt 1996). Several refugia have been tionary biologists. Unlike the limitations of inferred for many species in the Eurasian fossil records, phylogeographic studies continent, including those in Iberian, Ital- allow inferences of the demographics and ian and Balkan peninsulas (Hewitt 2000; evolutionary relationships among species Provan & Bennett 2008). These refugia based on genetic markers, and thus, have were geographically